3ZBF
Structure of Human ROS1 Kinase Domain in Complex with Crizotinib
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2XP2 | PDB ENTRY 2XP2 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 286 | CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION METHOD AT 13 DEGREES C BY MIXING 1.5 MICROLITERS OF SOLUTION CONTAINING A 1:3 MOLAR RATIO OF PHOSPHORYLATED ROS1 KD (12.2MG/ML) TO CRIZOTINIB AND 1.5 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 25% (W/V) PEG 3350, 0.6M POTASSIUM THIOCYANATE AND 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE, PH5.6. CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN AFTER TRANSFER TO 2 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 25% (V/V) GLYCEROL AS A CRYOPROTECTANT. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.74 | 55.1 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 106.854 | ¦Á = 90 |
b = 106.854 | ¦Â = 90 |
c = 50.357 | ¦Ã = 120 |
Symmetry | |
---|---|
Space Group | P 64 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 87 | CCD | MARRESEARCH | 2012-05-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | CLSI | 08ID-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.12 | 50 | 100 | 0.06 | 31 | 7.88 | 18796 | 33.9 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.12 | 2.2 | 100 | 0.59 | 3.7 | 7.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2XP2 | 2.2 | 44.23 | 16863 | 16486 | 796 | 97.7 | 0.236 | 0.233 | 0.282 | RANDOM | 52.5 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.63 | 2.53 | -1.63 | 3.26 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.2 |
c_scangle_it | 3.22 |
c_mcangle_it | 2.66 |
c_scbond_it | 2.24 |
c_mcbond_it | 1.63 |
c_angle_deg | 0.9 |
c_improper_angle_d | 0.67 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2260 |
Nucleic Acid Atoms | |
Solvent Atoms | 137 |
Heterogen Atoms | 30 |
Software
Software | |
---|---|
Software Name | Purpose |
CNX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNX | phasing |